RetrogeneDB ID: retro_cjac_3939

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: GL286347.1:16212..16846(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCJAG00000033949
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FXN
• Ensembl ID: ENSCJAG00000001695
• Aliases: None
• Description: frataxin [Source:HGNC Symbol;Acc:3951]

Sequence

>retro_cjac_3939
ATGTGGACTCTTGGCCACCACGCAGCCGCCGCCTTCCTACTCTGGTCGTCGTCCCCTAGCCCGGCCCAGGCCCAGACCGT
CGCCGGGGCCCCGTGGCCAGGGGAGTTGGCCCAGCTCTGCAGCCACTGCAGCCTGCACACCGGAATCGCAGAGGCCTGTG
GGTCACGTCACGCCAGTTTGAATCTTCATGGCCTCAACCAGATTCAGAATGTCAAAAGCAGAGTGTCTATTTGATGAATT
TGAGGAAAATGGGAACTTTGGGTCACCCAGGGTCTCTAGATGAGACCACCTGTGAAAGACTAGCAGAGGAAATGCTGGAC
TCCTTAGCTGAGTTTTTTGAAGACCTTGCAGACAAGCCATACATATTTGAAGACTATGATGTTTCTTTTGGGAGTGGTGT
CTTAAGTGTTAAACTGGGTGGAGATCTCGGAACTTAGGTATCAACAAGCAGACAGCAAACAAGCAAATCTGGCTATGTTC
TCCATCCAGTGGACCCAAGTGTTATGACTGGACTGGGAAAAGCTGGGTATACTCCCACGACGGCGTGTCCCTCCATGAGC
TGCTGGCCGCAGAGCTCACTAAAGCCTTAAAAACCAAACTGGACTTGTCTTCCTTGGCCTATTCTGGAAAAGAC

Alignment

ORF - retro_cjac_3939 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.58 %
• Parental protein coverage: 99.53 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MWTLGRRSAAGFLLWPSYTSPAQVQTVTRAPRPGELAQLCDCRALHTGIAKICASRHASLNLRGLNQIQN
          MWTLG...AA.FLLW.S..SPAQ.QTV..AP.PGELAQLC....LHTGIA..C.SRHASLNL.GLNQIQN
Retrocopy MWTLGHHAAAAFLLWSSSPSPAQAQTVAGAPWPGELAQLCSHCSLHTGIAEACGSRHASLNLHGLNQIQN

Parental  VK-KQSAYLMNLRKTGTLGHPGSLDETTYERLAEETLDSLAEFFEDLADKPYTFEDYDVSFGSGVLTVKL
          VK.KQS.YLMNLRK.GTLGHPGSLDETT.ERLAEE.LDSLAEFFEDLADKPY.FEDYDVSFGSGVL.VKL
Retrocopy VK<KQSVYLMNLRKMGTLGHPGSLDETTCERLAEEMLDSLAEFFEDLADKPYIFEDYDVSFGSGVLSVKL

Parental  GGDLGTYV-INKQTPNKQIWLSSPSSGPKRYDWTGKNWVYSHDGVSLHELLAAELTKALKTKLDLSYLAY
          GGDLGT.V.INKQT.NKQIWL.SPSSGPK.YDWTGK.WVYSHDGVSLHELLAAELTKALKTKLDLS.LAY
Retrocopy GGDLGT*V<INKQTANKQIWLCSPSSGPKCYDWTGKSWVYSHDGVSLHELLAAELTKALKTKLDLSSLAY

Parental  SGKD
          SGKD
Retrocopy SGKD

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP051959_colon	0.00 RPM	1.42 RPM
SRP051959_heart	0.00 RPM	4.24 RPM
SRP051959_kidney	0.02 RPM	3.37 RPM
SRP051959_liver	0.00 RPM	2.79 RPM
SRP051959_lung	0.05 RPM	2.38 RPM
SRP051959_lymph_node	0.05 RPM	1.48 RPM
SRP051959_skeletal_muscle	0.00 RPM	4.26 RPM
SRP051959_spleen	0.00 RPM	2.31 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_3939 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_3939 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_3939 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006915	1 retrocopy	retro_amel_1496,
Choloepus hoffmanni	ENSCHOG00000005107	2 retrocopies	retro_chof_349, retro_chof_94,
Callithrix jacchus	ENSCJAG00000001695	4 retrocopies	retro_cjac_1562, retro_cjac_1927, retro_cjac_3939 , retro_cjac_813,
Dasypus novemcinctus	ENSDNOG00000024066	3 retrocopies	retro_dnov_2204, retro_dnov_2317, retro_dnov_307,
Equus caballus	ENSECAG00000019174	1 retrocopy	retro_ecab_311,
Homo sapiens	ENSG00000165060	2 retrocopies	retro_hsap_1447, retro_hsap_4311,
Gorilla gorilla	ENSGGOG00000007636	3 retrocopies	retro_ggor_1112, retro_ggor_2203, retro_ggor_2881,
Macaca mulatta	ENSMMUG00000000357	2 retrocopies	retro_mmul_2038, retro_mmul_826,
Mustela putorius furo	ENSMPUG00000009619	2 retrocopies	retro_mputfur_501, retro_mputfur_803,
Mus musculus	ENSMUSG00000059363	2 retrocopies	retro_mmus_1571, retro_mmus_3058,
Otolemur garnettii	ENSOGAG00000031105	2 retrocopies	retro_ogar_1865, retro_ogar_476,
Rattus norvegicus	ENSRNOG00000015213	1 retrocopy	retro_rnor_2276,
Tursiops truncatus	ENSTTRG00000010336	4 retrocopies	retro_ttru_1281, retro_ttru_175, retro_ttru_546, retro_ttru_831,